Make multiple Bezier curves manifold and free of intersections, for 3D printing
I don't know what kind of mesh is needed for 3d printing, but I assume you want to remove the protruding faces from inside the face mesh. This should be possible with a script that would select the vertices of a mesh lying on one side of another mesh. Maybe someone can suggest a way to write such a script.

Here is a (rather tedious) workaround. 


In side view you do a cross section select by alt-b to select the upper part of the skull
you then box (or circle) select the vertices from inside
Turn the part round and deselect any vertices that might have got selected 
Do a delete face on all the selected vertices
Repeat this process to remove all the protruding faces of the hair mesh
Apply union modifier to create a single mesh out of the two parts


I guess (and I may be wrong), the hair part is already manifold, since the curve is converted to a surface.

Not sure if this would help you. But I am hoping to learn something myself by sharing my thoughts :)